Contacts of the helix formed by residues 150 - 159 (chain D) in PDB entry 1RFU
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASN 150 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117D GLY 2.6 28.4 - - - +
118D ASP* 3.9 6.6 - - - -
119D GLN* 3.3 33.6 + - - +
149D PRO* 1.3 74.3 - - - +
151D GLN* 1.3 56.3 + - - +
152D PHE* 4.2 2.7 - - - -
153D GLU* 2.7 33.1 + - + +
154D ALA* 2.4 36.5 + - - +
186D THR* 4.2 4.2 + - - -
3402D ADP 3.6 34.1 + - - -
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Residues in contact with GLN 151 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119D GLN* 3.1 28.2 - - - +
150D ASN* 1.3 73.6 - - - +
152D PHE* 1.3 53.9 + - - +
154D ALA* 3.1 3.5 + - - +
155D GLU* 2.6 61.9 + - - +
162D ILE* 4.0 27.4 + - + +
185D ILE* 3.8 11.3 - - + +
187D SER 3.2 14.5 + - - +
188D SER* 2.9 29.1 - - - -
189D ASN* 2.9 35.2 + - - +
190D LEU* 4.8 2.1 + - - +
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Residues in contact with PHE 152 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117D GLY* 3.6 31.4 - - - -
118D ASP 3.6 4.0 - - - -
119D GLN* 3.5 25.7 - - + +
124D GLY* 3.6 29.6 - - - -
125D ALA* 3.6 35.4 - - - -
126D MET* 3.7 11.9 - - + -
150D ASN* 3.0 4.5 - - - +
151D GLN* 1.3 79.5 - - - +
153D GLU* 1.3 66.8 + - + +
155D GLU* 3.0 21.5 + - - +
156D LEU* 2.7 43.7 + - + +
161D LYS* 5.6 5.8 - - - -
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Residues in contact with GLU 153 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113D ASP* 4.7 2.4 - - - +
114D PRO* 2.8 24.5 - - + +
115D VAL* 3.0 7.0 - - - +
116D MET* 2.6 33.4 + - + +
117D GLY 3.3 23.5 + - - +
127D TYR* 4.6 0.9 + - - -
148D THR 4.5 2.8 - - - +
149D PRO* 3.9 8.5 - - + +
150D ASN* 2.7 41.3 + - + +
152D PHE* 1.3 81.1 - - + +
154D ALA* 1.3 54.0 + - - +
156D LEU* 2.8 13.4 + - - +
157D LEU* 2.7 38.2 + - - +
3402D ADP 5.0 5.6 + - - -
3403D ZN 4.3 4.3 - - - -
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Residues in contact with ALA 154 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149D PRO* 3.9 12.0 - - + +
150D ASN 2.4 32.2 + - - +
151D GLN* 3.2 6.1 - - + +
153D GLU* 1.3 67.7 - - - +
155D GLU* 1.3 64.1 + - + +
157D LEU* 3.2 6.5 + - - +
158D THR* 3.0 25.2 + - - +
162D ILE* 5.9 2.5 - - + -
171D VAL* 3.7 13.7 - - + +
175D LEU* 4.6 2.0 - - + -
185D ILE* 3.4 31.4 - - + -
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Residues in contact with GLU 155 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123D GLU* 6.2 0.2 - - - +
151D GLN* 2.6 60.3 + - - +
152D PHE* 3.3 16.9 - - + +
154D ALA* 1.3 72.0 - - - +
156D LEU* 1.3 56.0 + - - +
158D THR* 3.2 5.3 + - - -
159D GLY* 2.7 32.4 + - - -
160D ARG 3.1 24.7 + - - +
161D LYS* 3.4 29.1 + - - +
162D ILE* 3.0 37.7 + - + +
171D VAL* 4.9 0.2 - - - +
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Residues in contact with LEU 156 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116D MET* 3.4 36.3 - - + -
126D MET* 3.9 24.0 - - + -
133D LEU* 3.4 38.8 - - + +
137D ARG* 4.6 3.1 + - - -
152D PHE* 2.7 36.1 + - + +
153D GLU* 2.8 17.2 + - - +
155D GLU* 1.3 78.3 - - - +
157D LEU* 1.3 59.4 + - - +
159D GLY* 3.6 8.3 + - - -
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Residues in contact with LEU 157 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114D PRO* 3.8 29.2 - - + -
116D MET* 3.6 21.8 - - + -
133D LEU* 4.2 3.1 - - + -
136D TYR* 4.1 15.0 - - + -
137D ARG* 3.2 40.7 - - + +
141D VAL* 4.1 26.7 - - + -
147D ILE* 5.3 2.5 - - + -
149D PRO* 4.4 4.9 - - + -
153D GLU 2.7 23.2 + - - +
154D ALA 3.8 2.7 - - - +
155D GLU 3.1 0.4 - - - -
156D LEU* 1.3 70.4 - - - +
158D THR* 1.3 59.2 + - - +
159D GLY 2.9 9.0 + - - -
175D LEU* 4.1 22.9 - - + -
178D MET* 4.6 7.3 - - - +
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Residues in contact with THR 158 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154D ALA 3.0 11.7 + - - -
155D GLU* 3.4 4.5 + - - -
157D LEU* 1.3 73.8 - - - +
159D GLY* 1.3 56.7 + - - +
160D ARG* 2.9 21.8 + - - +
171D VAL* 3.0 51.4 - - + +
174D MET* 3.5 34.9 - - + +
175D LEU* 3.5 17.7 - - + +
178D MET* 4.6 6.1 - - - -
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Residues in contact with GLY 159 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137D ARG* 5.9 2.2 - - - -
155D GLU 2.7 10.0 + - - -
156D LEU* 4.0 7.6 - - - -
157D LEU 2.9 6.6 + - - -
158D THR* 1.3 75.5 - - - +
160D ARG* 1.3 63.1 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il